Mon Sep 15 17:00:34 UTC 2025 I: starting to build biobambam2/forky/amd64 on jenkins on '2025-09-15 17:00' Mon Sep 15 17:00:34 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/69056/console.log Mon Sep 15 17:00:34 UTC 2025 I: Downloading source for forky/biobambam2=2.0.185+ds-2 --2025-09-15 17:00:34-- http://deb.debian.org/debian/pool/main/b/biobambam2/biobambam2_2.0.185%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2254 (2.2K) [text/prs.lines.tag] Saving to: ‘biobambam2_2.0.185+ds-2.dsc’ 0K .. 100% 265M=0s 2025-09-15 17:00:34 (265 MB/s) - ‘biobambam2_2.0.185+ds-2.dsc’ saved [2254/2254] Mon Sep 15 17:00:34 UTC 2025 I: biobambam2_2.0.185+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: biobambam2 Binary: biobambam2 Architecture: any Version: 2.0.185+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://gitlab.com/german.tischler/biobambam2 Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/biobambam2 Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev Package-List: biobambam2 deb science optional arch=any Checksums-Sha1: 2776b598958c159faa1147765a37a9be788c8725 249000 biobambam2_2.0.185+ds.orig.tar.xz a6d8b9f5865c14806d595f2ac8cd188e3f9edcd2 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Checksums-Sha256: 90cc8328f4e78771cf87cc918d890d12073cbbfbcad7cf94e35b655e3ec2747a 249000 biobambam2_2.0.185+ds.orig.tar.xz 5010ff92699f48db055e33a6ddda005ed339388cc1995503e985325e4d53652c 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Files: d0c485318daa583137b98d18fd0add77 249000 biobambam2_2.0.185+ds.orig.tar.xz bc64f60dd4ccfa2477438dcd2db1131e 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Dgit: 8e56855700614f8a0ddddf4fd2cb5611e10015e4 debian archive/debian/2.0.185+ds-2 https://git.dgit.debian.org/biobambam2 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmYikWMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrX1A//dGe1VAwa3juRlsGgmA9kRTYR+J89 x2/kBqtpIS8cO7onEyZ2MDixN7hFFq9QHCh0w7q1vBpdMMmPXJ5doQIQuTVcvWia Ugv0eGCk7v6Mja6dwECg9/JZ9IKn4BDQ0Mxectx/vWqEaa1BDhX4OLA6TfiluenO bYa0mcj4zm4jtlw1MbFYLOmf3d4fkSrDCtAqacc/DfchuesLVBkBaxb6oX/RuPzP T41aTROw4wxydmqd/04LSEXvJ55mZqzjihN+o12VpSsfdjsjQn/1WV9O7MmLbzdz VVDzXzOCrEzT0Um7E91gJ6E1D0RcUDlSCm2HXNcmUA2xc/ZawEQ8cOQMGkUao7NR DjeF38kGLokp/Djwd0LcoJDlIAfssb+T+B/gDndJINQpHzYsggCAlHfqjpJRRwpz CgvdGt2rrIi3ktmRoraoWmqN6XvCyjQFr3XxmLlw4T6p9Mk/5+Oj3IF+suMtm7EZ 1vLUbLoGwrT/zS+3Fdiu5+31uJv3Nm816IkefAEv/FhRqzrXW20IguFdmLFeQFI8 uP3+CcgbQfcs9REtB2MAJ50GQLi84ch3vXjxdizQAiZXgxhMNXXhn6BLNcgsYmVO 9v9u6mbo10JW+0kXVHsrg0f4I+OwdcrT/xuZKrsDM/VPgFdV6g+GQJE0Dkgbb6i2 py7JtzKEuhkACi0= =ZDUq -----END PGP SIGNATURE----- Mon Sep 15 17:00:34 UTC 2025 I: Checking whether the package is not for us Mon Sep 15 17:00:34 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Mon Sep 15 17:00:34 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Mon Sep 15 17:10:36 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 18 11:23:34 -12 2026 I: pbuilder-time-stamp: 1792365814 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biobambam2_2.0.185+ds-2.dsc] I: copying [./biobambam2_2.0.185+ds.orig.tar.xz] I: copying [./biobambam2_2.0.185+ds-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./biobambam2_2.0.185+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting biobambam2 in biobambam2-2.0.185+ds dpkg-source: info: unpacking biobambam2_2.0.185+ds.orig.tar.xz dpkg-source: info: unpacking biobambam2_2.0.185+ds-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3151147/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0662f3104a5342678c5ab209534f429a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3151147' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OXx6mqj2/pbuilderrc_L5Zp --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OXx6mqj2/b1 --logfile b1/build.log biobambam2_2.0.185+ds-2.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3151147/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libmaus2-dev (>= 2.0.800); however: Package libmaus2-dev is not installed. pbuilder-satisfydepends-dummy depends on libxerces-c-dev; however: Package libxerces-c-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libassuan9{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libelf1t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcrypt20{a} libgnutls30t64{a} libgpg-error0{a} libgpgme11t64{a} libgssapi-krb5-2{a} libicu-dev{a} libicu76{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libmaus2-2{a} libmaus2-dev{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnpth0t64{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxerces-c-dev{a} libxerces-c3.2t64{a} libxml2-16{a} m4{a} man-db{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl gnupg-utils gpg-wks-client gpgv gpgv-from-sq krb5-locales libarchive-cpio-perl libgpg-error-l10n libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 51.4 MB of archives. After unpacking 269 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 23 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libassuan9 amd64 3.0.2-2 [61.5 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 gpgconf amd64 2.4.8-3 [129 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libnpth0t64 amd64 1.8-3 [23.2 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 dirmngr amd64 2.4.8-3 [384 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 gnupg-l10n all 2.4.8-3 [753 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 gpg amd64 2.4.8-3 [634 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 pinentry-curses amd64 1.3.2-3 [87.8 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 gpg-agent amd64 2.4.8-3 [271 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 gpgsm amd64 2.4.8-3 [275 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 gnupg all 2.4.8-3 [418 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 60 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libgpgme11t64 amd64 1.24.2-3 [346 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get: 72 http://deb.debian.org/debian forky/main amd64 libmaus2-2 amd64 2.0.813+ds-4 [2073 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libmaus2-dev amd64 2.0.813+ds-4 [4688 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libxerces-c3.2t64 amd64 3.2.4+debian-1.3+b2 [898 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libxerces-c-dev amd64 3.2.4+debian-1.3+b2 [1708 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Fetched 51.4 MB in 0s (114 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... 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Preparing to unpack .../33-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package gpgconf. Preparing to unpack .../34-gpgconf_2.4.8-3_amd64.deb ... Unpacking gpgconf (2.4.8-3) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../35-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../36-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../37-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../38-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../39-libgnutls30t64_3.8.9-3_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.9-3) ... Selecting previously unselected package libksba8:amd64. Preparing to unpack .../40-libksba8_1.6.7-2+b1_amd64.deb ... Unpacking libksba8:amd64 (1.6.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../41-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... 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Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../55-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../56-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../57-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../58-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../59-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. 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Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../66-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../67-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../68-libcurl3t64-gnutls_8.15.0-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.15.0-1) ... Selecting previously unselected package libgpgme11t64:amd64. Preparing to unpack .../69-libgpgme11t64_1.24.2-3_amd64.deb ... Unpacking libgpgme11t64:amd64 (1.24.2-3) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../70-libicu-dev_76.1-4_amd64.deb ... Unpacking libicu-dev:amd64 (76.1-4) ... Selecting previously unselected package libmaus2-2:amd64. Preparing to unpack .../71-libmaus2-2_2.0.813+ds-4_amd64.deb ... Unpacking libmaus2-2:amd64 (2.0.813+ds-4) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../72-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libmaus2-dev. Preparing to unpack .../73-libmaus2-dev_2.0.813+ds-4_amd64.deb ... Unpacking libmaus2-dev (2.0.813+ds-4) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../74-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package libxerces-c3.2t64:amd64. Preparing to unpack .../75-libxerces-c3.2t64_3.2.4+debian-1.3+b2_amd64.deb ... Unpacking libxerces-c3.2t64:amd64 (3.2.4+debian-1.3+b2) ... Selecting previously unselected package libxerces-c-dev:amd64. Preparing to unpack .../76-libxerces-c-dev_3.2.4+debian-1.3+b2_amd64.deb ... Unpacking libxerces-c-dev:amd64 (3.2.4+debian-1.3+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../77-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../78-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libnpth0t64:amd64 (1.8-3) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libgpg-error0:amd64 (1.55-2) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libgcrypt20:amd64 (1.11.2-2) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up gnupg-l10n (2.4.8-3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libassuan9:amd64 (3.0.2-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libicu76:amd64 (76.1-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:amd64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.2-3) ... Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up icu-devtools (76.1-4) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up gpgconf (2.4.8-3) ... Setting up libicu-dev:amd64 (76.1-4) ... Setting up gpg (2.4.8-3) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up gpg-agent (2.4.8-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up gpgsm (2.4.8-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.4.8-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up gnupg (2.4.8-3) ... Setting up libgpgme11t64:amd64 (1.24.2-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libmaus2-2:amd64 (2.0.813+ds-4) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up debhelper (13.26) ... Setting up libxerces-c3.2t64:amd64 (3.2.4+debian-1.3+b2) ... Setting up libxerces-c-dev:amd64 (3.2.4+debian-1.3+b2) ... Setting up libmaus2-dev (2.0.813+ds-4) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/biobambam2-2.0.185+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biobambam2_2.0.185+ds-2_source.changes dpkg-buildpackage: info: source package biobambam2 dpkg-buildpackage: info: source version 2.0.185+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_auto_clean rm -f config.log make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:2: warning: The macro 'AC_CANONICAL_SYSTEM' is obsolete. configure.ac:2: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:2: the top level configure.ac:3: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:3: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:3: the top level configure.ac:6: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:6: You should use the 'AC_CONFIG_HEADERS' macro instead. aclocal.m4:1051: AM_CONFIG_HEADER is expanded from... configure.ac:6: the top level configure.ac:9: warning: The macro 'AC_CANONICAL_SYSTEM' is obsolete. configure.ac:9: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:9: the top level configure.ac:68: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:68: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... configure.ac:68: the top level configure.ac:147: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:147: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:147: the top level configure.ac:464: warning: AC_OUTPUT should be used without arguments. configure.ac:464: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for gawk... no checking for mawk... mawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether we are cross compiling... no checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking dependency style of g++... none checking whether the C++ compiler supports the -fsanitize=address flag... yes configure: Adding optimisation options -O3 to C compiler gcc flags, full list now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 configure: Adding optimisation options -O3 to C++ compiler g++ flags, full list now -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for egrep... (cached) /usr/bin/grep -E checking for libmaus2 >= 2.0.800... yes checking whether we can compile a program using libmaus2... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE_NP... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE... yes checking whether libmaus2 has support for io_lib... no checking for bash... /usr/bin/bash checking for base64... /usr/bin/base64 checking for xerces-c >= 3.1.1... yes configure: Using flags -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 for C compiler gcc configure: Using flags -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 for C++ compiler g++ checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating src/biobambam2/BamBamConfig.hpp config.status: creating config.h config.status: executing libtool commands config.status: executing depfiles commands dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make all-recursive make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making all in src make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamtofastq-bamtofastq.o `test -f 'programs/bamtofastq.cpp' || echo './'`programs/bamtofastq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicates-bammarkduplicates.o `test -f 'programs/bammarkduplicates.cpp' || echo './'`programs/bammarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsort-bamsort.o `test -f 'programs/bamsort.cpp' || echo './'`programs/bamsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammaskflags-bammaskflags.o `test -f 'programs/bammaskflags.cpp' || echo './'`programs/bammaskflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammaskflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrecompress-bamrecompress.o `test -f 'programs/bamrecompress.cpp' || echo './'`programs/bamrecompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrecompress-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamadapterfind-bamadapterfind.o `test -f 'programs/bamadapterfind.cpp' || echo './'`programs/bamadapterfind.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterfind-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterfind-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterfind-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilteraux-bamfilteraux.o `test -f 'programs/bamfilteraux.cpp' || echo './'`programs/bamfilteraux.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilteraux-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamauxsort-bamauxsort.o `test -f 'programs/bamauxsort.cpp' || echo './'`programs/bamauxsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamadapterclip-bamadapterclip.o `test -f 'programs/bamadapterclip.cpp' || echo './'`programs/bamadapterclip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterclip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterclip-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamcollate2-bamcollate2.o `test -f 'programs/bamcollate2.cpp' || echo './'`programs/bamcollate2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcollate2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcollate2-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcollate2-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bam12auxmerge-bam12auxmerge.o `test -f 'programs/bam12auxmerge.cpp' || echo './'`programs/bam12auxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bam12split-bam12split.o `test -f 'programs/bam12split.cpp' || echo './'`programs/bam12split.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12split-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12split-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bam12strip-bam12strip.o `test -f 'programs/bam12strip.cpp' || echo './'`programs/bam12strip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12strip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12strip-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamreset-bamreset.o `test -f 'programs/bamreset.cpp' || echo './'`programs/bamreset.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreset-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreset-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrank-bamrank.o `test -f 'programs/bamrank.cpp' || echo './'`programs/bamrank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrank-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrank-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamclipreinsert-bamclipreinsert.o `test -f 'programs/bamclipreinsert.cpp' || echo './'`programs/bamclipreinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamclipreinsert-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamclipreinsert-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamclipXT-bamclipXT.o `test -f 'programs/bamclipXT.cpp' || echo './'`programs/bamclipXT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamclipXT-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamzztoname-bamzztoname.o `test -f 'programs/bamzztoname.cpp' || echo './'`programs/bamzztoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamzztoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamzztoname-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamindex-bamindex.o `test -f 'programs/bamindex.cpp' || echo './'`programs/bamindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterflags-bamfilterflags.o `test -f 'programs/bamfilterflags.cpp' || echo './'`programs/bamfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterrg-bamfilterrg.o `test -f 'programs/bamfilterrg.cpp' || echo './'`programs/bamfilterrg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterrg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdownsamplerandom-bamdownsamplerandom.o `test -f 'programs/bamdownsamplerandom.cpp' || echo './'`programs/bamdownsamplerandom.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdownsamplerandom-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicates2-bammarkduplicates2.o `test -f 'programs/bammarkduplicates2.cpp' || echo './'`programs/bammarkduplicates2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicates2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamcat-bamcat.o `test -f 'programs/bamcat.cpp' || echo './'`programs/bamcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammerge-bammerge.o `test -f 'programs/bammerge.cpp' || echo './'`programs/bammerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsplit-bamsplit.o `test -f 'programs/bamsplit.cpp' || echo './'`programs/bamsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastsplit-bamfastsplit.o `test -f 'programs/bamfastsplit.cpp' || echo './'`programs/bamfastsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsplitdiv-bamsplitdiv.o `test -f 'programs/bamsplitdiv.cpp' || echo './'`programs/bamsplitdiv.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsplitdiv-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamchecksort-bamchecksort.o `test -f 'programs/bamchecksort.cpp' || echo './'`programs/bamchecksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamchecksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastqtobam-fastqtobam.o `test -f 'programs/fastqtobam.cpp' || echo './'`programs/fastqtobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixmateinformation-bamfixmateinformation.o `test -f 'programs/bamfixmateinformation.cpp' || echo './'`programs/bamfixmateinformation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixmateinformation-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamseqchksum-bamseqchksum.o `test -f 'programs/bamseqchksum.cpp' || echo './'`programs/bamseqchksum.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamseqchksum-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/normalisefasta-normalisefasta.o `test -f 'programs/normalisefasta.cpp' || echo './'`programs/normalisefasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/normalisefasta-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterheader-bamfilterheader.o `test -f 'programs/bamfilterheader.cpp' || echo './'`programs/bamfilterheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterheader2-bamfilterheader2.o `test -f 'programs/bamfilterheader2.cpp' || echo './'`programs/bamfilterheader2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterheader2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammdnm-bammdnm.o `test -f 'programs/bammdnm.cpp' || echo './'`programs/bammdnm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammdnm-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammapdist-bammapdist.o `test -f 'programs/bammapdist.cpp' || echo './'`programs/bammapdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammapdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamvalidate-bamvalidate.o `test -f 'programs/bamvalidate.cpp' || echo './'`programs/bamvalidate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamvalidate-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamflagsplit-bamflagsplit.o `test -f 'programs/bamflagsplit.cpp' || echo './'`programs/bamflagsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamflagsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamintervalcomment-bamintervalcomment.o `test -f 'programs/bamintervalcomment.cpp' || echo './'`programs/bamintervalcomment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamintervalcomment-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamintervalcommenthist-bamintervalcommenthist.o `test -f 'programs/bamintervalcommenthist.cpp' || echo './'`programs/bamintervalcommenthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamintervalcommenthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o `test -f 'programs/bamstreamingmarkduplicates.cpp' || echo './'`programs/bamstreamingmarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamstreamingmarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamalignfrac-bamalignfrac.o `test -f 'programs/bamalignfrac.cpp' || echo './'`programs/bamalignfrac.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamalignfrac-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilternames-bamfilternames.o `test -f 'programs/bamfilternames.cpp' || echo './'`programs/bamfilternames.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilternames-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsormadup-bamsormadup.o `test -f 'programs/bamsormadup.cpp' || echo './'`programs/bamsormadup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsormadup-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexplode-bamexplode.o `test -f 'programs/bamexplode.cpp' || echo './'`programs/bamexplode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexplode-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexploderef-bamexploderef.o `test -f 'programs/bamexploderef.cpp' || echo './'`programs/bamexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastexploderef-bamfastexploderef.o `test -f 'programs/bamfastexploderef.cpp' || echo './'`programs/bamfastexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastnumextract-bamfastnumextract.o `test -f 'programs/bamfastnumextract.cpp' || echo './'`programs/bamfastnumextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastnumextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamranksort-bamranksort.o `test -f 'programs/bamranksort.cpp' || echo './'`programs/bamranksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamranksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastaexplod-fastaexplod.o `test -f 'programs/fastaexplod.cpp' || echo './'`programs/fastaexplod.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastaexplod-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrecalculatecigar-bamrecalculatecigar.o `test -f 'programs/bamrecalculatecigar.cpp' || echo './'`programs/bamrecalculatecigar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrecalculatecigar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfiltermc-bamfiltermc.o `test -f 'programs/bamfiltermc.cpp' || echo './'`programs/bamfiltermc.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfiltermc-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamnumericalindex-bamnumericalindex.o `test -f 'programs/bamnumericalindex.cpp' || echo './'`programs/bamnumericalindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamnumericalindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamnumericalindexstats-bamnumericalindexstats.o `test -f 'programs/bamnumericalindexstats.cpp' || echo './'`programs/bamnumericalindexstats.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamnumericalindexstats-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicatesopt-bammarkduplicatesopt.o `test -f 'programs/bammarkduplicatesopt.cpp' || echo './'`programs/bammarkduplicatesopt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicatesopt-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterlength-bamfilterlength.o `test -f 'programs/bamfilterlength.cpp' || echo './'`programs/bamfilterlength.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterlength-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamauxmerge-bamauxmerge.o `test -f 'programs/bamauxmerge.cpp' || echo './'`programs/bamauxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrefinterval-bamrefinterval.o `test -f 'programs/bamrefinterval.cpp' || echo './'`programs/bamrefinterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrefinterval-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamscrapcount-bamscrapcount.o `test -f 'programs/bamscrapcount.cpp' || echo './'`programs/bamscrapcount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamscrapcount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterrefid-bamfilterrefid.o `test -f 'programs/bamfilterrefid.cpp' || echo './'`programs/bamfilterrefid.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterrefid-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfillquery-bamfillquery.o `test -f 'programs/bamfillquery.cpp' || echo './'`programs/bamfillquery.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfillquery-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfillquery-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrefextract-bamrefextract.o `test -f 'programs/bamrefextract.cpp' || echo './'`programs/bamrefextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrefextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastqtobam2-fastqtobam2.o `test -f 'programs/fastqtobam2.cpp' || echo './'`programs/fastqtobam2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam2-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamauxmerge2-bamauxmerge2.o `test -f 'programs/bamauxmerge2.cpp' || echo './'`programs/bamauxmerge2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxmerge2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxmerge2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamreheader-bamreheader.o `test -f 'programs/bamreheader.cpp' || echo './'`programs/bamreheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamreplacechecksums-bamreplacechecksums.o `test -f 'programs/bamreplacechecksums.cpp' || echo './'`programs/bamreplacechecksums.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastcat-bamfastcat.o `test -f 'programs/bamfastcat.cpp' || echo './'`programs/bamfastcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastcat-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp programs/fastqtobam2.cpp: In member function 'virtual void BlockReadControl::checkBgzfWriteQueue()': programs/fastqtobam2.cpp:3861:43: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3861 | while ( ptr = bgzfGetNext() ) | ^ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastcat-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/populaterefcache-populaterefcache.o `test -f 'programs/populaterefcache.cpp' || echo './'`programs/populaterefcache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/populaterefcache-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfiltereofblocks-bamfiltereofblocks.o `test -f 'programs/bamfiltereofblocks.cpp' || echo './'`programs/bamfiltereofblocks.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfiltereofblocks-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfiltereofblocks-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdepth-bamdepth.o `test -f 'programs/bamdepth.cpp' || echo './'`programs/bamdepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdepthintersect-bamdepthintersect.o `test -f 'programs/bamdepthintersect.cpp' || echo './'`programs/bamdepthintersect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepthintersect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepthintersect-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterk-bamfilterk.o `test -f 'programs/bamfilterk.cpp' || echo './'`programs/bamfilterk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterk-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterk-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterk-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixpairinfo-bamfixpairinfo.o `test -f 'programs/bamfixpairinfo.cpp' || echo './'`programs/bamfixpairinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixpairinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixpairinfo-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixpairinfo-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdifference-bamdifference.o `test -f 'programs/bamdifference.cpp' || echo './'`programs/bamdifference.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdifference-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfeaturecount-bamfeaturecount.o `test -f 'programs/bamfeaturecount.cpp' || echo './'`programs/bamfeaturecount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfeaturecount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/blastnxmltobam-blastnxmltobam.o `test -f 'programs/blastnxmltobam.cpp' || echo './'`programs/blastnxmltobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/blastnxmltobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilter-bamfilter.o `test -f 'programs/bamfilter.cpp' || echo './'`programs/bamfilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilter-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterbyname-bamfilterbyname.o `test -f 'programs/bamfilterbyname.cpp' || echo './'`programs/bamfilterbyname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterbyname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixmatecoordinates-bamfixmatecoordinates.o `test -f 'programs/bamfixmatecoordinates.cpp' || echo './'`programs/bamfixmatecoordinates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixmatecoordinates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o `test -f 'programs/bamfixmatecoordinatesnamesorted.cpp' || echo './'`programs/bamfixmatecoordinatesnamesorted.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamtoname-bamtoname.o `test -f 'programs/bamtoname.cpp' || echo './'`programs/bamtoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamtoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdisthist-bamdisthist.o `test -f 'programs/bamdisthist.cpp' || echo './'`programs/bamdisthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdisthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastabgzfextract-fastabgzfextract.o `test -f 'programs/fastabgzfextract.cpp' || echo './'`programs/fastabgzfextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastabgzfextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheap-bamheap.o `test -f 'programs/bamheap.cpp' || echo './'`programs/bamheap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfrontback-bamfrontback.o `test -f 'programs/bamfrontback.cpp' || echo './'`programs/bamfrontback.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfrontback-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfrontback-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrandomtag-bamrandomtag.o `test -f 'programs/bamrandomtag.cpp' || echo './'`programs/bamrandomtag.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrandomtag-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheap2-bamheap2.o `test -f 'programs/bamheap2.cpp' || echo './'`programs/bamheap2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheap2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheap3-bamheap3.o `test -f 'programs/bamheap3.cpp' || echo './'`programs/bamheap3.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheap3-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamtagconversion-bamtagconversion.o `test -f 'programs/bamtagconversion.cpp' || echo './'`programs/bamtagconversion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamtagconversion-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastqtobampar-fastqtobampar.o `test -f 'programs/fastqtobampar.cpp' || echo './'`programs/fastqtobampar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobampar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bambisect-bambisect.o `test -f 'programs/bambisect.cpp' || echo './'`programs/bambisect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bambisect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcffilterinfo-vcffilterinfo.o `test -f 'programs/vcffilterinfo.cpp' || echo './'`programs/vcffilterinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcffilterinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o `test -f 'programs/vcfpatchcontigprepend.cpp' || echo './'`programs/vcfpatchcontigprepend.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfpatchcontigprepend-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfconcat-vcfconcat.o `test -f 'programs/vcfconcat.cpp' || echo './'`programs/vcfconcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfconcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfsort-vcfsort.o `test -f 'programs/vcfsort.cpp' || echo './'`programs/vcfsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/filtergtf-filtergtf.o `test -f 'programs/filtergtf.cpp' || echo './'`programs/filtergtf.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/filtergtf-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamconsensus-bamconsensus.o `test -f 'programs/bamconsensus.cpp' || echo './'`programs/bamconsensus.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamconsensus-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfreplacecontigs-vcfreplacecontigs.o `test -f 'programs/vcfreplacecontigs.cpp' || echo './'`programs/vcfreplacecontigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfreplacecontigs-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcffiltersamples-vcffiltersamples.o `test -f 'programs/vcffiltersamples.cpp' || echo './'`programs/vcffiltersamples.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcffiltersamples-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexploderg-bamexploderg.o `test -f 'programs/bamexploderg.cpp' || echo './'`programs/bamexploderg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexploderg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexondepth-bamexondepth.o `test -f 'programs/bamexondepth.cpp' || echo './'`programs/bamexondepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexondepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexondepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp In file included from programs/bamexondepth.cpp:22: ./biobambam2/DepthIntervalGetter.hpp: In member function 'uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)': ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable 'HE' [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ In file included from /usr/include/c++/15/cassert:46, from /usr/include/libmaus2/avl/AVLSet.hpp:24, from programs/bamexondepth.cpp:43: programs/bamexondepth.cpp: In function 'void handleFile(const std::string&, uint64_t, const libmaus2::bambam::BamHeader&, std::ostream&, std::ostream&, const std::string&)': programs/bamexondepth.cpp:121:44: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] 121 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ programs/bamexondepth.cpp:371:32: warning: comparison of integer expressions of different signedness: 'const uint64_t' {aka 'const long unsigned int'} and 'int64_t' {aka 'long int'} [-Wsign-compare] 371 | if ( d <= thresdepth ) | ~~^~~~~~~~~~~~~ programs/bamexondepth.cpp:375:52: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] 375 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheadercat-bamheadercat.o `test -f 'programs/bamheadercat.cpp' || echo './'`programs/bamheadercat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheadercat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o `test -f 'programs/bammarkduplicatesoptdist.cpp' || echo './'`programs/bammarkduplicatesoptdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicatesoptdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfdiff-vcfdiff.o `test -f 'programs/vcfdiff.cpp' || echo './'`programs/vcfdiff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfdiff-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsimpledepth-bamsimpledepth.o `test -f 'programs/bamsimpledepth.cpp' || echo './'`programs/bamsimpledepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsimpledepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsimpledepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdepthmerge-bamdepthmerge.o `test -f 'programs/bamdepthmerge.cpp' || echo './'`programs/bamdepthmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepthmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamcountflags-bamcountflags.o `test -f 'programs/bamcountflags.cpp' || echo './'`programs/bamcountflags.cpp In file included from programs/bamdepthmerge.cpp:23: ./biobambam2/DepthIntervalGetter.hpp: In member function 'uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)': ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable 'HE' [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcountflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcffilterfilterflags-vcffilterfilterflags.o `test -f 'programs/vcffilterfilterflags.cpp' || echo './'`programs/vcffilterfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcffilterfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o `test -f 'programs/vcfreplacecontigsmap.cpp' || echo './'`programs/vcfreplacecontigsmap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfreplacecontigsmap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastaselectreg-fastaselectreg.o `test -f 'programs/fastaselectreg.cpp' || echo './'`programs/fastaselectreg.cpp programs/vcfreplacecontigsmap.cpp:29:12: warning: 'int getDefaultGZ()' defined but not used [-Wunused-function] 29 | static int getDefaultGZ() { return 0; } | ^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastaselectreg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamaddne-bamaddne.o `test -f 'programs/bamaddne.cpp' || echo './'`programs/bamaddne.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamaddne-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamadapterhistogram-bamadapterhistogram.o `test -f 'programs/bamadapterhistogram.cpp' || echo './'`programs/bamadapterhistogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterhistogram-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsalvage-bamsalvage.o `test -f 'programs/bamsalvage.cpp' || echo './'`programs/bamsalvage.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsalvage-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamtofastq-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool 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-Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreset programs/bamreset-bamreset.o biobambam2/bamreset-Licensing.o biobambam2/bamreset-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrank programs/bamrank-bamrank.o biobambam2/bamrank-Licensing.o biobambam2/bamrank-AttachRank.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamzztoname programs/bamzztoname-bamzztoname.o biobambam2/bamzztoname-Licensing.o biobambam2/bamzztoname-zzToName.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamclipXT programs/bamclipXT-bamclipXT.o biobambam2/bamclipXT-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 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-fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterrg programs/bamfilterrg-bamfilterrg.o biobambam2/bamfilterrg-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdownsamplerandom programs/bamdownsamplerandom-bamdownsamplerandom.o biobambam2/bamdownsamplerandom-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamindex programs/bamindex-bamindex.o biobambam2/bamindex-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterflags programs/bamfilterflags-bamfilterflags.o biobambam2/bamfilterflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastaexplod programs/fastaexplod-fastaexplod.o biobambam2/fastaexplod-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecalculatecigar programs/bamrecalculatecigar-bamrecalculatecigar.o biobambam2/bamrecalculatecigar-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecalculatecigar programs/bamrecalculatecigar-bamrecalculatecigar.o biobambam2/bamrecalculatecigar-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfiltermc programs/bamfiltermc-bamfiltermc.o biobambam2/bamfiltermc-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamnumericalindex programs/bamnumericalindex-bamnumericalindex.o biobambam2/bamnumericalindex-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamnumericalindexstats programs/bamnumericalindexstats-bamnumericalindexstats.o biobambam2/bamnumericalindexstats-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterlength programs/bamfilterlength-bamfilterlength.o biobambam2/bamfilterlength-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxmerge programs/bamauxmerge-bamauxmerge.o biobambam2/bamauxmerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterlength programs/bamfilterlength-bamfilterlength.o biobambam2/bamfilterlength-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamnumericalindexstats programs/bamnumericalindexstats-bamnumericalindexstats.o biobambam2/bamnumericalindexstats-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge programs/bamauxmerge-bamauxmerge.o biobambam2/bamauxmerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrefinterval programs/bamrefinterval-bamrefinterval.o biobambam2/bamrefinterval-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamscrapcount programs/bamscrapcount-bamscrapcount.o biobambam2/bamscrapcount-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterrefid programs/bamfilterrefid-bamfilterrefid.o biobambam2/bamfilterrefid-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfillquery programs/bamfillquery-bamfillquery.o biobambam2/bamfillquery-Licensing.o 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge2 programs/bamauxmerge2-bamauxmerge2.o biobambam2/bamauxmerge2-Licensing.o biobambam2/bamauxmerge2-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterrefid programs/bamfilterrefid-bamfilterrefid.o biobambam2/bamfilterrefid-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreplacechecksums programs/bamreplacechecksums-bamreplacechecksums.o biobambam2/bamreplacechecksums-Licensing.o biobambam2/bamreplacechecksums-ReadHeader.o biobambam2/bamreplacechecksums-RunEOFFilter.o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now 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-ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfiltereofblocks programs/bamfiltereofblocks-bamfiltereofblocks.o biobambam2/bamfiltereofblocks-Licensing.o biobambam2/bamfiltereofblocks-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepthintersect programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o blastnxmltobam programs/blastnxmltobam-blastnxmltobam.o biobambam2/blastnxmltobam-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz -lxerces-c libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastcat programs/bamfastcat-bamfastcat.o biobambam2/bamfastcat-Licensing.o biobambam2/bamfastcat-ReadHeader.o biobambam2/bamfastcat-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o populaterefcache programs/populaterefcache-populaterefcache.o biobambam2/populaterefcache-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfiltereofblocks programs/bamfiltereofblocks-bamfiltereofblocks.o biobambam2/bamfiltereofblocks-Licensing.o biobambam2/bamfiltereofblocks-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepthintersect programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o blastnxmltobam programs/blastnxmltobam-blastnxmltobam.o biobambam2/blastnxmltobam-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -lxerces-c -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepthmerge programs/bamdepthmerge-bamdepthmerge.o biobambam2/bamdepthmerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterfilterflags programs/vcffilterfilterflags-vcffilterfilterflags.o biobambam2/vcffilterfilterflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigsmap programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o biobambam2/vcfreplacecontigsmap-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtofastq programs/bamtofastq-bamtofastq.o biobambam2/bamtofastq-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicates programs/bammarkduplicates-bammarkduplicates.o biobambam2/bammarkduplicates-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepth programs/bamdepth-bamdepth.o 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-ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterhistogram programs/bamadapterhistogram-bamadapterhistogram.o biobambam2/bamadapterhistogram-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterhistogram programs/bamadapterhistogram-bamadapterhistogram.o biobambam2/bamadapterhistogram-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making all in test make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making check in src make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making check in test make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make bamcmp bamtosam make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o bamcmp-bamcmp.o `test -f 'bamcmp.cpp' || echo './'`bamcmp.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o bamtosam-bamtosam.o `test -f 'bamtosam.cpp' || echo './'`bamtosam.cpp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtosam bamtosam-bamtosam.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtosam bamtosam-bamtosam.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcmp bamcmp-bamcmp.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcmp bamcmp-bamcmp.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make check-TESTS make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[4]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' PASS: testshortsortcoordinate.sh PASS: testshortsortqueryname.sh PASS: testshortsort.sh PASS: testdupsinglemarkedsortedqreset.sh PASS: testdupsingle.sh PASS: testfastqbamloop.sh ============================================================================ Testsuite summary for biobambam2 2.0.185 ============================================================================ # TOTAL: 6 # PASS: 6 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/biobambam2/ make -j1 install DESTDIR=/build/reproducible-path/biobambam2-2.0.185\+ds/debian/biobambam2 AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making install in src make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' /usr/bin/mkdir -p '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress bamadapterfind bamfilteraux bamauxsort bamadapterclip bamcollate2 bam12auxmerge bam12split bam12strip bamreset bamrank bamclipreinsert bamclipXT bamzztoname bamindex bamfilterflags bamfilterrg bamdownsamplerandom bammarkduplicates2 bamcat bammerge bamsplit bamfastsplit bamsplitdiv bamchecksort fastqtobam bamfixmateinformation bamseqchksum normalisefasta bamfilterheader bamfilterheader2 bammdnm bammapdist bamvalidate bamflagsplit bamintervalcomment bamintervalcommenthist bamstreamingmarkduplicates bamalignfrac bamfilternames bamsormadup bamexplode bamexploderef bamfastexploderef bamfastnumextract bamranksort fastaexplod bamrecalculatecigar bamfiltermc bamnumericalindex bamnumericalindexstats bammarkduplicatesopt bamfilterlength bamauxmerge bamrefinterval bamscrapcount bamfilterrefid bamfillquery bamrefextract fastqtobam2 bamauxmerge2 bamreheader bamreplacechecksums bamfastcat populaterefcache bamfiltereofblocks bamdepth bamdepthintersect bamfilterk bamfixpairinfo bamdifference bamfeaturecount '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin' libtool: install: /usr/bin/install -c bamtofastq /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamtofastq libtool: install: /usr/bin/install -c bammarkduplicates /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicates libtool: install: /usr/bin/install -c bamsort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsort libtool: install: /usr/bin/install -c bammaskflags /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammaskflags libtool: install: /usr/bin/install -c bamrecompress /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrecompress libtool: install: /usr/bin/install -c bamadapterfind /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamadapterfind libtool: install: /usr/bin/install -c bamfilteraux /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilteraux libtool: install: /usr/bin/install -c bamauxsort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxsort libtool: install: /usr/bin/install -c bamadapterclip /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamadapterclip libtool: install: /usr/bin/install -c bamcollate2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamcollate2 libtool: install: /usr/bin/install -c bam12auxmerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12auxmerge libtool: install: /usr/bin/install -c bam12split /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12split libtool: install: /usr/bin/install -c bam12strip /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12strip libtool: install: /usr/bin/install -c bamreset /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreset libtool: install: /usr/bin/install -c bamrank /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrank libtool: install: /usr/bin/install -c bamclipreinsert /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamclipreinsert libtool: install: /usr/bin/install -c bamclipXT /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamclipXT libtool: install: /usr/bin/install -c bamzztoname /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamzztoname libtool: install: /usr/bin/install -c bamindex /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamindex libtool: install: /usr/bin/install -c bamfilterflags /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterflags libtool: install: /usr/bin/install -c bamfilterrg /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterrg libtool: install: /usr/bin/install -c bamdownsamplerandom /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdownsamplerandom libtool: install: /usr/bin/install -c bammarkduplicates2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicates2 libtool: install: /usr/bin/install -c bamcat /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamcat libtool: install: /usr/bin/install -c bammerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammerge libtool: install: /usr/bin/install -c bamsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsplit libtool: install: /usr/bin/install -c bamfastsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastsplit libtool: install: /usr/bin/install -c bamsplitdiv /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsplitdiv libtool: install: /usr/bin/install -c bamchecksort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamchecksort libtool: install: /usr/bin/install -c fastqtobam /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastqtobam libtool: install: /usr/bin/install -c bamfixmateinformation /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfixmateinformation libtool: install: /usr/bin/install -c bamseqchksum /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamseqchksum libtool: install: /usr/bin/install -c normalisefasta /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/normalisefasta libtool: install: /usr/bin/install -c bamfilterheader /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterheader libtool: install: /usr/bin/install -c bamfilterheader2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterheader2 libtool: install: /usr/bin/install -c bammdnm /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammdnm libtool: install: /usr/bin/install -c bammapdist /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammapdist libtool: install: /usr/bin/install -c bamvalidate /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamvalidate libtool: install: /usr/bin/install -c bamflagsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamflagsplit libtool: install: /usr/bin/install -c bamintervalcomment /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamintervalcomment libtool: install: /usr/bin/install -c bamintervalcommenthist /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamintervalcommenthist libtool: install: /usr/bin/install -c bamstreamingmarkduplicates /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamstreamingmarkduplicates libtool: install: /usr/bin/install -c bamalignfrac /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamalignfrac libtool: install: /usr/bin/install -c bamfilternames /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilternames libtool: install: /usr/bin/install -c bamsormadup /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsormadup libtool: install: /usr/bin/install -c bamexplode /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamexplode libtool: install: /usr/bin/install -c bamexploderef /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamexploderef libtool: install: /usr/bin/install -c bamfastexploderef /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastexploderef libtool: install: /usr/bin/install -c bamfastnumextract /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastnumextract libtool: install: /usr/bin/install -c bamranksort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamranksort libtool: install: /usr/bin/install -c fastaexplod /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastaexplod libtool: install: /usr/bin/install -c bamrecalculatecigar /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrecalculatecigar libtool: install: /usr/bin/install -c bamfiltermc /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfiltermc libtool: install: /usr/bin/install -c bamnumericalindex /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamnumericalindex libtool: install: /usr/bin/install -c bamnumericalindexstats /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamnumericalindexstats libtool: install: /usr/bin/install -c bammarkduplicatesopt /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicatesopt libtool: install: /usr/bin/install -c bamfilterlength /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterlength libtool: install: /usr/bin/install -c bamauxmerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxmerge libtool: install: /usr/bin/install -c bamrefinterval /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrefinterval libtool: install: /usr/bin/install -c bamscrapcount /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamscrapcount libtool: install: /usr/bin/install -c bamfilterrefid /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterrefid libtool: install: /usr/bin/install -c bamfillquery /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfillquery libtool: install: /usr/bin/install -c bamrefextract /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrefextract libtool: install: /usr/bin/install -c fastqtobam2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastqtobam2 libtool: install: /usr/bin/install -c bamauxmerge2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxmerge2 libtool: install: /usr/bin/install -c bamreheader /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreheader libtool: install: /usr/bin/install -c bamreplacechecksums /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreplacechecksums libtool: install: /usr/bin/install -c bamfastcat /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastcat libtool: install: /usr/bin/install -c populaterefcache /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/populaterefcache libtool: install: /usr/bin/install -c bamfiltereofblocks /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfiltereofblocks libtool: install: /usr/bin/install -c bamdepth /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdepth libtool: install: /usr/bin/install -c bamdepthintersect /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdepthintersect libtool: install: /usr/bin/install -c bamfilterk /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterk libtool: install: /usr/bin/install -c bamfixpairinfo /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfixpairinfo libtool: install: /usr/bin/install -c bamdifference /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdifference libtool: install: /usr/bin/install -c bamfeaturecount /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfeaturecount /usr/bin/mkdir -p '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/bamtofastq.1 programs/bamsort.1 programs/bammarkduplicates.1 programs/bammarkduplicatesopt.1 programs/bammaskflags.1 programs/bamrecompress.1 programs/bamadapterfind.1 programs/bamfilteraux.1 programs/bamauxsort.1 programs/bamadapterclip.1 programs/bamcollate2.1 programs/bam12auxmerge.1 programs/bam12split.1 programs/bam12strip.1 programs/bamreset.1 programs/bamrank.1 programs/bamclipreinsert.1 programs/bamzztoname.1 programs/bamindex.1 programs/bamfilterflags.1 programs/bamfilterrg.1 programs/bamdownsamplerandom.1 programs/bammarkduplicates2.1 programs/bamcat.1 programs/bammerge.1 programs/bamsplit.1 programs/bamsplitdiv.1 programs/bamchecksort.1 programs/fastqtobam.1 programs/bamfixmateinformation.1 programs/normalisefasta.1 programs/bamfilterheader.1 programs/bamfilterheader2.1 programs/bammdnm.1 programs/bamseqchksum.1 programs/bamvalidate.1 programs/bamflagsplit.1 programs/bamintervalcomment.1 programs/bamstreamingmarkduplicates.1 programs/bamsormadup.1 '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/fastaexplod.1 programs/bamrecalculatecigar.1 programs/bamfiltermc.1 programs/bamfillquery.1 programs/bamalignfrac.1 programs/bamauxmerge.1 programs/bamauxmerge2.1 programs/bambisect.1 programs/bamclipXT.1 programs/bamconsensus.1 programs/filtergtf.1 programs/bamfeaturecount.1 '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making install in test make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamfilterheader were not linked against libmaus2_simd_align_128.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamrefextract debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamfilterheader were not linked against libmaus2_simd_align_256.so.2 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'biobambam2' in '../biobambam2_2.0.185+ds-2_amd64.deb'. dpkg-deb: building package 'biobambam2-dbgsym' in '../biobambam2-dbgsym_2.0.185+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../biobambam2_2.0.185+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../biobambam2_2.0.185+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3151147 and its subdirectories I: Current time: Sun Oct 18 11:33:33 -12 2026 I: pbuilder-time-stamp: 1792366413 Mon Sep 15 17:10:36 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Mon Sep 15 17:10:36 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Mon Sep 15 17:18:29 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Mon Sep 15 17:18:29 UTC 2025 I: biobambam2_2.0.185+ds-2_amd64.changes: Format: 1.8 Date: Fri, 19 Apr 2024 17:24:26 +0200 Source: biobambam2 Binary: biobambam2 biobambam2-dbgsym Architecture: amd64 Version: 2.0.185+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: biobambam2 - tools for early stage alignment file processing Changes: biobambam2 (2.0.185+ds-2) unstable; urgency=medium . * d/watch: repair gitlab watch file. This instructs uscan to use git ls-remote mode. * d/control: declare compliance to standards version 4.7.0. * d/control: move from pkg-config to pkgconf. Checksums-Sha1: eea1b1f17fbc1c60fea5232b633be1d1943558f2 225753652 biobambam2-dbgsym_2.0.185+ds-2_amd64.deb 18acd344d860c08d06f14c461caabaa20ad9695e 6638 biobambam2_2.0.185+ds-2_amd64.buildinfo 9fa4028975c5bc14377936401f1d5e16054a3010 10180056 biobambam2_2.0.185+ds-2_amd64.deb Checksums-Sha256: bb077010876349f2138859ab5ab5e2f278f2bde61eaacf55fa57410ad1e761cd 225753652 biobambam2-dbgsym_2.0.185+ds-2_amd64.deb 973cba24a22a483fc1e007dff0dee345b678c3756a194af43e6f169897119618 6638 biobambam2_2.0.185+ds-2_amd64.buildinfo a59c60a24fd21a44493e872a275c36de8a12db4742769aefe6715320d369a53d 10180056 biobambam2_2.0.185+ds-2_amd64.deb Files: 7cdba9b243e23182107f5dc1e209463b 225753652 debug optional biobambam2-dbgsym_2.0.185+ds-2_amd64.deb 0bc8eae18402b98078805dfc288c4572 6638 science optional biobambam2_2.0.185+ds-2_amd64.buildinfo 6a9a30ba442b945fcb1c74dddb36c475 10180056 science optional biobambam2_2.0.185+ds-2_amd64.deb Mon Sep 15 17:18:30 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-69056.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OXx6mqj2/biobambam2_2.0.185+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OXx6mqj2/biobambam2_2.0.185+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OXx6mqj2/biobambam2_2.0.185+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OXx6mqj2/b1/biobambam2_2.0.185+ds-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.OXx6mqj2/b2/biobambam2_2.0.185+ds-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 246ms CPU time consumed: 186ms Memory peak: 18.8M (swap: 0B) Mon Sep 15 17:20:51 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Mon Sep 15 17:20:51 UTC 2025 I: biobambam2 from forky built successfully and reproducibly on amd64. Mon Sep 15 17:20:53 UTC 2025 I: Removing signed biobambam2_2.0.185+ds-2_amd64.buildinfo.asc files: removed './b1/biobambam2_2.0.185+ds-2_amd64.buildinfo.asc' removed './b2/biobambam2_2.0.185+ds-2_amd64.buildinfo.asc'